Publications & Presentations

Publications

All publications

LaVerriere, Emily et al.

Sept 2026.

Open Forum Infectious Diseases.

Genomic surveillance uncovers a shift in respiratory syncytial virus subtype dominance and the local expansion of subclade B.D.E.1.7.

Krasilnikova, Lydia A. et al.

May 2026.

medRxiv

Genomic epidemiology as a tool for understanding drivers of hepatitis A community outbreaks in Massachusetts and New Hampshire.

Kalinich, Chaney C. et al.

Feb 2026.

Journal of Clinical Microbiology.

A tiled amplicon protocol for culture-free whole-genome sequencing of M. tuberculosis from clinical specimens.

Adams, Gordon C. et al.

Dec 2025.

Open Forum Infectious Diseases.

Development of a Combined Clinical and Research-Developed Testing Strategy for Highly Pathogenic Avian Influenza A Virus H5.

LaVerriere, Emily et al.

June 2025.

Open Forum Infectious Diseases.

Genomic Epidemiology of Respiratory Syncytial Virus in a New England Hospital System, 2024.

Varilly, Patrick et al.

Mar 2025.

bioRxiv.

Delphy: scalable, near-real-time Bayesian phylogenetics for outbreaks.

Specht, Ivan et al.

Mar 2025.

medRxiv.

JUNIPER: Reconstructing Transmission Events from Next-Generation Sequencing Data at Scale.

Moreno, Gage K. et al.

Apr 2025.

medRxiv.

Genomic surveillance reveals age-structured transmission across demographics and settings.

Stachler, Elyse et al.

Mar 2025.

Emerging Infectious Diseases.

Establishing methods to monitor H5N1 influenza virus in dairy cattle milk.

Roster, Kirstin I. Oliveira et al.

Dec 2024.

American Journal of Epidemiology.

Estimating the undetected burden of infections and the likelihood of strain persistence of drug-resistant Neisseria gonorrhoeae.

Roster, Kirstin I. Oliveira et al.

Aug 2024.

The Lancet Infectious Diseases.

Modelling molecular and culture-based surveillance of tetracycline resistance in Neisseria gonorrhoeae.

Palace, Samantha G. et al.

Aug 2024.

medRxiv.

An updated molecular diagnostic for surveillance of tetM in Neisseria gonorrhoeae.

Paull, Jillian S. et al.

May 2024.

The Lancet Microbe.

Optimisation and evaluation of viral genomic sequencing of SARS-CoV-2 rapid diagnostic tests: a laboratory and cohort-based study.

Hume, Adam J. et al.

Jan 2024.

Pathogens.

Heat Inactivation of Nipah Virus for Downstream Single-Cell RNA Sequencing Does Not Interfere with Sample Quality.

Libuit, Kevin G. et al.

Jul 2023.

Microbial Genomics.

Accelerating bioinformatics implementation in public health.

Adams, Gordon et al.

Feb 2023.

The New England Journal of Medicine.

Viral lineages in the 2022 RSV surge in the United States.

Presentations

Tools for Applying the phylosamp Sample Size Framework to Improve Variant Surveillance in a Public Health Setting

CSTE Annual Conference 2026

Carolyn Casiello

5/31/2026-6/6/2026

Genomics for Public Health Action: A Case Study in Hepatitis A Whole-Genome Sequencing and Genomic Epidemiology

CSTE Annual Conference 2026

Emily Decker

5/31/2026-6/6/2026

Developing a Notification Protocol for High Priority Pathogens Identified with Metagenomic Sequencing

CSTE Annual Conference 2026

Meagan Burns

5/31/2026-6/6/2026

Applying a sample size calculation framework to evaluate and improve SARS-CoV-2 variant surveillance in Massachusetts

CSTE Annual Conference 2025

Carolyn Casiello

6/8/2025-6/12/2025

Updates from the Pathogen Genomics Centers of Excellence: advances in AMD driven by academic-public health partnership

APHL Annual Conference 2025

Betsy Osborn

5/7/25

Workplace Development panel

AMD Days 2024

Betsy Osborn

View

Study design considerations for genomic epidemiology

AMD Days 2024

Shirlee Wohl

9/24/24

2024 NE PGCoE Annual Symposium

9/11/24

Posters

Tools for Applying the phylosamp Sample Size Framework to Improve Variant Surveillance in a Public Health Setting

APHL Annual Conference 2026

Zack Thompson

5/4/2026-5/7/2026

Novel Hepatitis A Genotyping Tools for Public Health Laboratories

APHL Annual Conference 2026

Mary Godec

5/4/2026-5/7/2026

Hybrid Capture Pathogen Sequencing for Routine and Outbreak Surveillance

APHL Annual Conference 2026

Emily Dart

5/4/2026-5/7/2026

Amplicon-Based Whole-Genome Sequencing of Mycobacterium tuberculosis

Applied Bioinformatics & Public Health Microbiology Annual Conference 2025

Seth Redmond

5/21/2025-5/23/2025

Applying a sample size calculation framework to evaluate and improve SARS-CoV-2 variant surveillance in Massachusetts, APHL Annual Conference 2025

APHL Annual Conference 2025

Zack Thompson

5/8/2025-5/23/2025

Hybrid capture for whole genome sequencing: rabies as a test case

AMD Days 2024

Emily Dart

9/23/2024-9/24/2024

Development of a whole-genome sequencing data integration strategy: incorporating enteric disease sequencing results with epidemiologic case data in Massachusetts

AMD Days 2024

Emily Decker

9/23/2024-9/24/2024

PGCoE in the News